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- PDB-1egi: STRUCTURE OF A C-TYPE CARBOHYDRATE-RECOGNITION DOMAIN (CRD-4) FRO... -

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Basic information

Entry
Database: PDB / ID: 1egi
TitleSTRUCTURE OF A C-TYPE CARBOHYDRATE-RECOGNITION DOMAIN (CRD-4) FROM THE MACROPHAGE MANNOSE RECEPTOR
ComponentsMACROPHAGE MANNOSE RECEPTOR
KeywordsSUGAR BINDING PROTEIN / C-type lectin / mannose receptor
Function / homology
Function and homology information


cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Ricin B, lectin domain / Ricin B-like lectins / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Kringle-like fold / Roll / Alpha Beta
Similarity search - Domain/homology
Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsFeinberg, H. / Park-Snyder, S. / Kolatkar, A.R. / Heise, C.T. / Taylor, M.E. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor.
Authors: Feinberg, H. / Park-Snyder, S. / Kolatkar, A.R. / Heise, C.T. / Taylor, M.E. / Weis, W.I.
History
DepositionFeb 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MACROPHAGE MANNOSE RECEPTOR
B: MACROPHAGE MANNOSE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7215
Polymers33,6012
Non-polymers1203
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.056, 38.689, 55.025
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MACROPHAGE MANNOSE RECEPTOR


Mass: 16800.596 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE-RECOGNITION DOMAIN 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22897
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8-13% polyethylene glycol, 100 mM Tris pH 8.0, 100 mM NaCl, 10 mM CaCl2, 100 mM a-Me-Man. The crystals were then transferred to a solution containing 200 mM methyl 3-O-(a-D-mannopyranosyl)-a- ...Details: 8-13% polyethylene glycol, 100 mM Tris pH 8.0, 100 mM NaCl, 10 mM CaCl2, 100 mM a-Me-Man. The crystals were then transferred to a solution containing 200 mM methyl 3-O-(a-D-mannopyranosyl)-a-D-mannopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
23-5 mM1dropCaCl2
38-13 %PEG100001reservoir
4100 mMTris1reservoir
5100 mM1reservoirNaCl
610 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 12333 / Num. obs: 12246 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.354 / Num. unique all: 603 / % possible all: 100
Reflection
*PLUS
Num. measured all: 103297
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.3→500 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 766262.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1200 10.4 %RANDOM
Rwork0.212 ---
obs-11589 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.19 Å20 Å2-1.09 Å2
2--1.23 Å20 Å2
3----8.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 3 115 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.552
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 192 10.6 %
Rwork0.26 1612 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.26

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